A Software article published in MicrobiomeJ introduces LotuS2: a tool designed to improve the reproducibility, accuracy and ease of amplicon sequencing analysis. Read the article:
Based on the mock community data, LotuS2 was more precise in the reported 16S rRNA gene sequences, assigning the correct taxonomy, and detecting biodiversity. Within-genome 16S copies were less likely to be clustered separately using LotuS2.LotuS2 offers a fast, accurate, and streamlined amplicon data analysis with new features and substantial improvements since LotuS1. Software and workflow optimizations make LotuS2 substantially faster than all QIIME 2, DADA2, and mothur.
LotuS2 owes high reproducibility and accuracy to the efficient use of reads based on their quality tiers in different steps of the pipeline. Low-quality reads introduce noise and can artificially inflate observed biodiversity, i.e., the number of OTUs/ASVs []. Conversely, an overly strict read filter will decrease sensitivity for low-abundant members of a community by artificially reducing sequencing depth.
Notably, OTUs/ASVs reported with LotuS2 were the most similar to the reference, compared to other pipelines . This was mostly independent of clustering algorithms used, rather resulting from a combination of selecting high-quality reads for sequence clustering and the seed extension step selecting a high-quality read best representing each OTU or ASV.
In conclusion, LotuS2 is a major improvement over LotuS1, representing pipeline updates that accumulated over the past 8 years. It offers superior computational performance, accuracy, and reproducibility of results, compared to the other tested pipelines. Importantly, it is straightforward to install, and programmed to reduce required user time and knowledge, following the idea that “less is more with LotuS2”.
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